Genomic and phenotypic improvement of triticale (×Triticosecale Wittmack) line and hybrid breeding programs

Triticale (×Triticosecale Wittmack) breeding is a success story as it evolved to a serious alternative in farmers crop rotations since the 1970s and is grown globally on around 4 million hectares today. New developments, however, pointed out additional possibilities to improve triticale line and hybrid breeding programs increasing its future competitiveness and were evaluated in this study. In more detail, these were to (i) examine the genetic control and evaluate long term genetic trends of plant height in Central European winter triticale, (ii) evaluate the potential of triticale hybrid breeding and hybrid prediction approaches in triticale with a focus on biomass yield, (iii) introduce and examine a concept bypassing the time and resource consuming evaluation of female candidate lines in cytoplasmatic male sterility (CMS) based hybrid breeding, and (iv) to draw conclusions for the future improvement of triticale line and hybrid breeding programs. The genome wide association study detected markers significantly associated with plant height and developmental stage, respectively. These explained 42,16% and 29,31% of the total genotypic variance of plant height and development stage and are probably related to four and three quantitative trait loci (QTL), respectively. The two major QTL detected for plant height were located on chromosomes 5A and 5R which most likely could be assigned to the known height reducing genes Rht12 from wheat and Ddw1 from rye. The third major QTL detected located on chromosome 4B could not be assigned to a known height reducing gene and it cannot be precluded, that these significantly associated markers are identifying one and the same QTL as the markers located on chromosome 5R, as these showed a high linkage disequilibrium amongst each other. Evaluating the 129 registered cultivars showed that plant height decreased since the 1980s. Evaluating their genetic constitution revealed that most cultivars carried at least one height reducing QTL and that plant height could be reduced even further in cultivars combining more than one height reducing QTL. It was further observed that the frequency of cultivars carrying one or a combination of height reducing QTL increased since the 1980s. A considerable amount of heterosis has been observed for biomass related traits in triticale hybrids before. However, the use of hybrid prediction approaches for these traits has not been evaluated. Hybrid prediction based on mid parent values already showed very good results illustrating their potential to preselect the most promising parents as prediction accuracies based on parental general combining ability (GCA) effects were only slightly better. When incorporating molecular markers into GCA based prediction accuracies, prediction accuracies decreased slightly compared to prediction accuracies solely based on phenotypic GCA effects. Predicting hybrids incorporating one or two untested parental lines, imitating a scenario where novel female and/or male candidate lines are introduced into a hybrid breeding program, reduced genomic prediction accuracies even further due to the decreasing amount of information which could be exploited from the parents. Additionally including specific combining ability (SCA) effects in the genomic prediction models did not yield additional use. A high proportion of SCA variance compared to the total genetic variance decreased prediction accuracies for the traits fresh and dry biomass yield. In this study simulation studies were used to demonstrate what a prediction accuracy of a specific value actually means for a hybrid breeding programs. Further, an approach was introduced and evaluated showing great potential to evaluate novel female candidate lines for their use in a CMS based hybrid breeding program by bypassing their time and resource demanding introgression into a male sterile cytoplasm using three way hybrids. Prediction accuracies obtained by this novel approach showed highly promising results for most evaluated traits compared to prediction accuracies based on GCA effects or mid parent performance. Additionally incorporating SCA effects into the prediction models showed only a little increase of the prediction accuracies. Further, the results were supported by simulation studies adjusting different parameters, such as the number of parents or the proportion of SCA variance compared to the total genetic variance.Die Züchtung von Triticale (×Triticosecale Wittmack) ist eine Erfolgsgeschichte, da sie sich seit den 1970er Jahren zu einer ernstzunehmenden Alternative in der Fruchtfolge von Landwirten entwickelt hat und heute weltweit auf rund 4 Millionen Hektar angebaut wird. Jüngere Entwicklungen jedoch identifizierten zusätzliches Potential zur Verbesserung von Triticale Linien und Hybridzüchtungsprogrammen, die die Konkurrenzfähigkeit von Triticale weiter erhöhen können und wurden deshalb in dieser Studie näher beleuchtet. Genauer betrachtet waren die Ziele dieser Studie (i) die genetische Struktur und genetischen Langzeittrends des Merkmals Wuchshöhe in Mitteleuropäischer Wintertriticale zu untersuchen, (ii) die Potenziale der Hybridzüchtung und Konzepte zur Hybridvorhersage in Triticale, mit dem Fokus auf Biomasseertrag, zu evaluieren, (iii) ein Konzept, welches die zeit und ressourcenintensive Beurteilung weiblicher Mutterkomponenten in der zytoplasmatisch männlich sterilen (CMS) Hybridzüchtung vereinfacht, vorzustellen sowie bezüglich seiner Zweckdienlichkeit zu bewerten, und (iv) um Rückschlüsse für die zukünftige Verbesserung von Triticale Linien und Hybridzuchtprogrammen zu ziehen. In einer genomweiten Assoziationsstudie wurden Marker entdeckt, die signifikant mit den Merkmalen Wuchshöhe und Entwicklungsstadium assoziiert waren. Diese erklärten 42,16% beziehungsweise 29,31% der Gesamtvarianz der genannten Merkmale und repräsentieren wahrscheinlich vier beziehungsweise drei merkmalsbeeinflussende Genorte (QTL). Es wurden zwei bedeutende QTL für das Merkmal Wuchshöhe auf den Chromosomen 5A und 5R entdeckt, welche höchstwahrscheinlich den Wuchshöhe reduzierenden Genen Rht12 von Weizen und Ddw1 von Roggen zuzuschreiben sind. Das dritte bedeutende QTL, welches auf Chromosom 4B gefunden wurde, konnte keinem bekannten Wuchshöhe reduzierenden Gen zugeordnet werden. Ferner kann nicht ausgeschlossen werden, dass diese als signifikant identifizierten Marker ein und dasselbe QTL identifizieren, wie die auf Chromosom 5R liegenden Marker, da diese untereinander ein hohes Kopplungsungleichgewicht aufweisen. Die Wuchshöhe der 129 untersuchten zugelassenen Sorten nahm seit den 1980er Jahren kontinuierlich ab. Die Untersuchung der zugrunde liegenden genetischen Ursachen hat ergeben, dass die meisten Sorten mindestens ein Wuchshöhereduzierendes QTL trugen und dass sich die Wuchshöhe noch weiter verringerte, wenn eine Sorte mehrere Wuchshöhe reduzierende Gene vereinte. Außerdem konnte beobachtet werden, dass sich seit den 1980er Jahren die Häufigkeit von zugelassenen Sorten die ein oder eine Kombination aus mehreren Wuchshöhe reduzierenden QTL trugen erhöht hat. Ein beträchtlicher Umfang an Heterosis wurde in früheren Studien für Biomassemerkmale beobachtet. Nichtsdestotrotz wurden die Nützlichkeit von Hybridvorhersageansätzen bisher nicht evaluiert. Hybridvorhersagen, welche auf dem Mittelwert ihrer Elternlinien basieren zeigten vielversprechende Vorhersagegenauigkeiten und spiegelte somit ihr hohes Potential für die Vorselektion der vielversprechendsten Elternkomponenten wider, da Vorhersagegenauigkeiten basierend auf den elterlichen allgemeinen Kombinationsfähigkeiten (GCA) nur geringfügig besser waren. Mit der Aufnahme von molekularen Markerdaten in die GCA basierten Vorhersagen verringerten sich die Vorhersagegenauigkeiten im Vergleich zu den Vorhersagen, welche lediglich auf phänotypischen GCA Effekten basierten. Bei Vorhersagen, welche ein oder zwei ungetestete Elternlinien beinhalteten, d.h. in einem Szenario welches neue weibliche und/oder männliche Kandidatenlinien in ein Hybridzuchtprogramm integriert, verringerten sich die genomischen Vorhersagegenauigkeiten noch weiter, da nur von einem beziehungsweise von keinem Elter Information genutzt werden konnte. Die zusätzliche Einbeziehung von spezifischen Kombinationseffekten (SCA) in die genomischen Vorhersagemodelle ergab keinen zusätzlichen Nutzen. Ein hoher Anteil an SCA Varianz an der genetischen Gesamtvarianz verringerte die Vorhersagegenauigkeiten für die Merkmale Frisch und Trockenbiomasseertrag. Ferner wurde anhand von Simulationsstudien abgeleitet, was eine bestimmte Vorhersagegenauigkeit eigentlich für ein Hybridzüchtungsprogramm bedeutet. Es wurde ein neuer Ansatz auf seinen Nutzen in einem CMS basierten Hybridzuchtprogram hin evaluiert der die zeit und ressourcenintensive Rückkreuzung weiblicher Kandidatenlinien für deren Evaluierung in ein männlich steriles Zytoplasma umgeht. Die durch diesen neuen Ansatz erhaltenen Vorhersagegenauigkeiten zeigten großes Potential für die meisten untersuchten Merkmale im Vergleich zu Vorhersagegenauigkeiten basierend auf GCA Werten oder ihrem elterlichen Mittelwert. Das zusätzliche Miteinbeziehen von SCA Effekten in die Vorhersagemodelle zeigte nur eine geringfügige Verbesserung der Vorhersagegenauigkeiten. Außerdem konnten die Ergebnisse durch Simulationsstudien unter Anpassung verschiedener Parameter, wie die Anzahl der Eltern oder der Anteil der SCA Varianz an der genetischen Gesamtvarianz, untermauert werden

Energy Estimation of Cosmic Rays with the Engineering Radio Array of the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA) is part of the Pierre Auger Observatory and is used to detect the radio emission of cosmic-ray air showers. These observations are compared to the data of the surface detector stations of the Observatory, which provide well-calibrated information on the cosmic-ray energies and arrival directions. The response of the radio stations in the 30 to 80 MHz regime has been thoroughly calibrated to enable the reconstruction of the incoming electric field. For the latter, the energy deposit per area is determined from the radio pulses at each observer position and is interpolated using a two-dimensional function that takes into account signal asymmetries due to interference between the geomagnetic and charge-excess emission components. The spatial integral over the signal distribution gives a direct measurement of the energy transferred from the primary cosmic ray into radio emission in the AERA frequency range. We measure 15.8 MeV of radiation energy for a 1 EeV air shower arriving perpendicularly to the geomagnetic field. This radiation energy -- corrected for geometrical effects -- is used as a cosmic-ray energy estimator. Performing an absolute energy calibration against the surface-detector information, we observe that this radio-energy estimator scales quadratically with the cosmic-ray energy as expected for coherent emission. We find an energy resolution of the radio reconstruction of 22% for the data set and 17% for a high-quality subset containing only events with at least five radio stations with signal.Comment: Replaced with published version. Added journal reference and DO

Measurement of the Radiation Energy in the Radio Signal of Extensive Air Showers as a Universal Estimator of Cosmic-Ray Energy

We measure the energy emitted by extensive air showers in the form of radio emission in the frequency range from 30 to 80 MHz. Exploiting the accurate energy scale of the Pierre Auger Observatory, we obtain a radiation energy of 15.8 \pm 0.7 (stat) \pm 6.7 (sys) MeV for cosmic rays with an energy of 1 EeV arriving perpendicularly to a geomagnetic field of 0.24 G, scaling quadratically with the cosmic-ray energy. A comparison with predictions from state-of-the-art first-principle calculations shows agreement with our measurement. The radiation energy provides direct access to the calorimetric energy in the electromagnetic cascade of extensive air showers. Comparison with our result thus allows the direct calibration of any cosmic-ray radio detector against the well-established energy scale of the Pierre Auger Observatory.Comment: Replaced with published version. Added journal reference and DOI. Supplemental material in the ancillary file

Multiple Scenario Generation of Subsurface Models:Consistent Integration of Information from Geophysical and Geological Data throuh Combination of Probabilistic Inverse Problem Theory and Geostatistics

Neutrinos with energies above 1017 eV are detectable with the Surface Detector Array of the Pierre Auger Observatory. The identification is efficiently performed for neutrinos of all flavors interacting in the atmosphere at large zenith angles, as well as for Earth-skimming \u3c4 neutrinos with nearly tangential trajectories relative to the Earth. No neutrino candidates were found in 3c 14.7 years of data taken up to 31 August 2018. This leads to restrictive upper bounds on their flux. The 90% C.L. single-flavor limit to the diffuse flux of ultra-high-energy neutrinos with an E\u3bd-2 spectrum in the energy range 1.0 7 1017 eV -2.5 7 1019 eV is E2 dN\u3bd/dE\u3bd < 4.4 7 10-9 GeV cm-2 s-1 sr-1, placing strong constraints on several models of neutrino production at EeV energies and on the properties of the sources of ultra-high-energy cosmic rays

Measurement of the Fluctuations in the Number of Muons in Extensive Air Showers with the Pierre Auger Observatory

The successful installation, commissioning, and operation of the Pierre Auger Observatory would not have been possible without the strong commitment and effort from the technical and administrative staff in Malargue. We are very grateful to the following agencies and organizations for financial support: Argentina-Comision Nacional de Energia Atomica, Agencia Nacional de Promocion Cientifica y Tecnologica (ANPCyT), Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Gobierno de la Provincia de Mendoza, Municipalidad de Malargue, NDM Holdings and Valle Las Lenas; in gratitude for their continuing cooperation over land access; Australia-the Australian Research Council; BrazilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Financiadora de Estudos e Projetos (FINEP), Fundacao de Amparo a Pesquisa do Estado de Rio de Janeiro (FAPERJ), Sao Paulo Research Foundation (FAPESP) Grants No. 2019/10151-2, No. 2010/07359-6, and No. 1999/05404-3, Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC); Ministry of Education, Youth and Sports of the Czech RepublicGrants No. MSMT CR LTT18004, No. LM2015038, No. LM2018102, No. CZ.02.1.01/0.0/0.0/16_013/0001402, No. CZ.02.1.01/0.0/0.0/18_046/0016010, and No. CZ.02.1.01/0.0/0.0/17_049/0008422; France-Centre de Calcul IN2P3/CNRS, Centre National de la Recherche Scientifique (CNRS), Conseil Regional Ile-de-France, Departement Physique Nucl ' eaire et Corpusculaire (PNC-IN2P3/CNRS), Departement Sciences de l'Univers (SDU-INSU/CNRS), Institut Lagrange de Paris (ILP) Grant No. LABEX ANR-10-LABX-63 within the Investissements d'Avenir Programme Grant No. ANR11-IDEX-0004-02; Germany-Bundesministerium fur Bildung und Forschung (BMBF), Deutsche Forschungsgemeinschaft (DFG), Finanzministerium Baden-Wurttemberg, Helmholtz Alliance for Astroparticle Physics (HAP), Helmholtz-Gemeinschaft Deutscher Forschungszentren (HGF), Ministerium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-Westfalen, Ministerium fur Wissenschaft, Forschung und Kunst des Landes Baden-Wurttemberg; Italy-Istituto Nazionale di Fisica Nucleare (INFN), Istituto Nazionale di Astrofisica (INAF), Ministero dell'Istruzione, dell'Universita e della Ricerca (MIUR), CETEMPS Center of Excellence, Ministero degli Affari Esteri (MAE); Mexico-Consejo Nacional de Ciencia y Tecnologia (CONACYT) Grant No. 167733, Universidad Nacional Autonoma de Mexico (UNAM), PAPIIT DGAPA-UNAM; The Netherlands-Ministry of Education, Culture and Science, Netherlands Organisation for Scientific Research (NWO), Dutch national e-infrastructure with the support of SURF Cooperative; Poland-Ministry of Science and Higher Education, Grant No. DIR/WK/2018/11, National Science Centre, Grants No. 2013/08/M/ST9/00322, No. 2016/23/B/ST9/01635, and No. HARMONIA 5-2013/10/M/ST9/00062, UMO-2016/22/M/ST9/00198; Portugal -Portuguese national funds and FEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE); Romania-Romanian Ministry of Education and Research, the Program Nucleu within MCI (PN19150201/16N/2019 and PN19060102), and project PN-III-P1-1.2-PCCDI-2017-0839/19PCCDI/2018 within PNCDI III; Slovenia-Slovenian Research Agency, Grants No. P1-0031, No. P1-0385, No. I00033, No. N1-0111; Spain-Ministerio de Economia, Industria y Competitividad (FPA2017-85114-P and FPA2017-85197-P), Xunta de Galicia (ED431C 2017/07), Junta de Andalucia (SOMM17/6104/UGR), Feder Funds, RENATA Red Nacional Tematica de Astroparticulas (FPA2015-68783-REDT), and Maria de Maeztu Unit of Excellence (MDM-2016-0692); U.S.Department of Energy, Awards No. DE-AC0207CH11359, No. DE-FR02-04ER41300, No. DE-FG0299ER41107, and No. DE-SC0011689, National Science Foundation, Grant No. 0450696, The Grainger Foundation, Marie Curie-IRSES/EPLANET, European Particle Physics Latin American Network, and UNESCO.We present the first measurement of the fluctuations in the number of muons in extensive air showers produced by ultrahigh energy cosmic rays. We find that the measured fluctuations are in good agreement with predictions from air shower simulations. This observation provides new insights into the origin of the previously reported deficit of muons in air shower simulations and constrains models of hadronic interactions at ultrahigh energies. Our measurement is compatible with the muon deficit originating from small deviations in the predictions from hadronic interaction models of particle production that accumulate as the showers develop.Argentina-Comision Nacional de Energia AtomicaANPCyTConsejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET)Gobierno de la Provincia de MendozaMunicipalidad de MalargueNDM HoldingsValle Las LenasAustralian Research CouncilConselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPQ)Fundacao de Apoio a Pesquisa do Distrito Federal (FAPDF)Financiadora de Inovacao e Pesquisa (Finep)Fundacao Carlos Chagas Filho de Amparo a Pesquisa do Estado do Rio De Janeiro (FAPERJ)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) 2019/10151-2 2010/07359-6 1999/05404-3Ministerio da Ciencia, Tecnologia, Inovacoes e Comunicacoes (MCTIC)Ministry of Education, Youth & Sports - Czech Republic MSMT CR LTT18004 LM2015038 LM2018102 CZ.02.1.01/0.0/0.0/16_013/0001402 CZ.02.1.01/0.0/0.0/18_046/0016010 CZ.02.1.01/0.0/0.0/17_049/0008422France-Centre de Calcul IN2P3/CNRSCentre National de la Recherche Scientifique (CNRS)Region Ile-de-FranceCentre National de la Recherche Scientifique (CNRS)Departement Sciences de l'Univers (SDU-INSU/CNRS)French National Research Agency (ANR) LABEX ANR-10-LABX-63 ANR11-IDEX-0004-02Federal Ministry of Education & Research (BMBF)German Research Foundation (DFG)Finanzministerium Baden-WurttembergHelmholtz Alliance for Astroparticle Physics (HAP)Helmholtz AssociationMinisterium fur Innovation, Wissenschaft und Forschung des Landes Nordrhein-WestfalenMinisterium fur Wissenschaft, Forschung und Kunst des Landes Baden-WurttembergItaly-Istituto Nazionale di Fisica Nucleare (INFN)Istituto Nazionale Astrofisica (INAF)Ministry of Education, Universities and Research (MIUR)CETEMPS Center of ExcellenceMinistry of Foreign Affairs and International Cooperation (Italy)Consejo Nacional de Ciencia y Tecnologia (CONACyT) 167733Universidad Nacional Autonoma de Mexico (UNAM), PAPIIT DGAPA-UNAMNetherlands-Ministry of Education, Culture and ScienceNetherlands Organization for Scientific Research (NWO)Dutch national e-infrastructureSURF CooperativePoland-Ministry of Science and Higher Education DIR/WK/2018/11National Science Centre, Poland 2013/08/M/ST9/00322 2016/23/B/ST9/01635 HARMONIA 5-2013/10/M/ST9/00062 UMO-2016/22/M/ST9/00198Portugal -Portuguese national fundsFEDER funds within Programa Operacional Factores de Competitividade through Fundacao para a Ciencia e a Tecnologia (COMPETE)Romania-Romanian Ministry of Education and Research, the Program Nucleu within MCI PN19150201/16N/2019 PN19060102Romania-Romanian Ministry of Educatio n and Research, the Program Nucleu within PNCDI III PN-III-P1-1.2-PCCDI-2017-0839/19PCCDI/2018Slovenian Research Agency - Slovenia P1-0031 P1-0385 I00033 N1-0111Spain-Ministerio de Economia, Industria y Competitividad FPA2017-85114-P FPA2017-85197-PXunta de Galicia European Commission ED431C 2017/07Junta de Andalucia SOMM17/6104/UGREuropean CommissionRENATA Red Nacional Tematica de Astroparticulas FPA2015-68783-REDTMaria de Maeztu Unit of Excellence MDM-2016-0692United States Department of Energy (DOE) DE-AC0207CH11359 DE-FR02-04ER41300 DE-FG0299ER41107 DE-SC0011689National Science Foundation (NSF) 0450696Grainger FoundationMarie Curie-IRSES/EPLANETEuropean Particle Physics Latin American NetworkUNESC

Erratum: Combined fit of spectrum and composition data as measured by the Pierre Auger Observatory

We present a combined fit of a simple astrophysical model of UHECR sources to both the energy spectrum and mass composition data measured by the Pierre Auger Observatory. The fit has been performed for energies above 5 ⋅ 10(18) eV, i.e. the region of the all-particle spectrum above the so-called ankle feature. The astrophysical model we adopted consists of identical sources uniformly distributed in a comoving volume, where nuclei are accelerated through a rigidity-dependent mechanism. The fit results suggest sources characterized by relatively low maximum injection energies, hard spectra and heavy chemical composition. We also show that uncertainties about physical quantities relevant to UHECR propagation and shower development have a non-negligible impact on the fit results